R Packages that start with:
A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .
Functions
- check_alignment()
- check_alignment_params()
- check_alignment_params_names()
- check_beast2_installed()
- check_candidates_save_to_same_files()
- check_error_fun()
- check_error_measure_params()
- check_experiment()
- check_experiments()
- check_experiments_all_inference_models_are_unique()
- check_experiments_candidates_have_same_mcmcs()
- check_gen_and_cand_exps_save_to_different_files()
- check_inference_conditions()
- check_inference_model_type_names()
- check_inference_model_weights()
- check_init_pir_params()
- check_is_ns_beast2_pkg_installed()
- check_model_type()
- check_mutation_rate()
- check_pir_out()
- check_pir_out_errors_above_zero()
- check_pir_out_names()
- check_pir_params()
- check_pir_paramses()
- check_pir_params_data_types()
- check_pir_params_names()
- check_reconstructed_phylogeny()
- check_root_sequence()
- check_sim_tral_fun()
- check_sim_twal_fun()
- check_sim_twin_tree_fun()
- check_tree_and_model()
- check_tree_and_models()
- check_tree_and_model_errors()
- check_tree_type()
- check_tree_types()
- check_twinning_params()
- check_twinning_params_names()
- check_twin_phylogeny()
- collapse_tree_and_model()
- collect_pir_outs()
- combine_brts_and_topology()
- combine_models()
- complete_treelog_filename()
- convert_pir_out_to_long()
- convert_tree2brts()
- copy_true_alignment()
- count_n_mutations()
- create_alignment_params()
- create_all_bd_experiments()
- create_all_coal_experiments()
- create_all_experiments()
- create_bd_tree()
- create_blocked_dna()
- create_cand_experiment()
- create_copy_twtr_from_true_fun()
- create_error_measure_params()
- create_exemplary_dd_tree()
- create_exemplary_dd_tree_giappo()
- create_experiment()
- create_gen_experiment()
- create_inference_conditions()
- create_mono_nuc_dna()
- create_pir_params()
- create_sim_yule_twin_tree_fun()
- create_standard_mutation_rate()
- create_std_pir_params()
- create_std_pir_paramses()
- create_test_alignment_params()
- create_test_cand_experiment()
- create_test_experiment()
- create_test_gen_experiment()
- create_test_marg_liks()
- create_test_phylogeny()
- create_test_pir_params()
- create_test_pir_params_setup()
- create_test_pir_run_output()
- create_test_pir_run_output2()
- create_tral_file()
- create_tree_and_model_errors_from_folder()
- create_tree_and_model_errors_from_folders()
- create_true_alignment()
- create_twal_file()
- create_twinning_params()
- create_twin_branching_times()
- create_twin_tree()
- create_yule_tree()
- default_params_doc()
- delete_beast2_state_files()
- errorses_to_data_frame()
- est_evidences()
- get_alignment_n_taxa()
- get_alignment_sequences()
- get_alignment_sequence_length()
- get_copy_tral_fun()
- get_experiments_filenames()
- get_experiment_filenames()
- get_gamma_error_fun()
- get_model_selections()
- get_model_type_names()
- get_nltt_error_fun()
- get_pir_params_filenames()
- get_pir_plot_fill_colors()
- get_pir_plot_line_colors()
- get_pir_plot_theme()
- get_pir_plot_tree_and_model_descriptions()
- get_remove_hex_twin_fun()
- get_sim_bd_twin_tree_fun()
- get_sim_tral_with_lns_nsm_fun()
- get_sim_tral_with_std_nsm_fun()
- get_sim_tral_with_uns_nsm_fun()
- get_sim_twal_same_n_muts_fun()
- get_sim_twal_with_std_nsm_fun()
- get_sim_yule_twin_tree_fun()
- get_temp_errors_filename()
- get_temp_evidence_filename()
- get_temp_fasta_filename()
- get_temp_tree_filename()
- get_test_alignment()
- get_tree_and_model_descriptions()
- get_tree_and_model_values()
- get_tree_types()
- get_twin_methods()
- get_twin_models()
- has_candidate_experiments()
- has_twinning()
- init_experiment()
- init_pir_params()
- is_best_candidate()
- is_dna_seq()
- is_pir_params()
- phylo_to_errors()
- pipe()
- pirouette()
- pir_plot()
- pir_plots()
- pir_plot_from_file()
- pir_plot_from_long()
- pir_rename()
- pir_rename_to_std()
- pir_run()
- pir_runs()
- pir_run_distribution()
- pir_run_true_tree()
- pir_run_twin_tree()
- pir_save()
- pir_to_pics()
- pir_to_tables()
- plot_alignment_from_file()
- read_errors_csv()
- relevel_inference_model()
- relevel_tree_and_model()
- renum_rng_seeds()
- replicate_pir_params()
- rm_pir_param_files()
- select_candidate_evidences()
- select_experiments()
- shorten_experiments()
- shorten_pir_params()
- shorten_pir_paramses()
- sim_alignment_with_n_mutations()
- sim_alignment_with_std_nsm()
- sim_alignment_with_std_nsm_from_params()
- sim_bd_twin_tree()
- sim_tral_with_lns_nsm()
- sim_tral_with_std_nsm()
- sim_tral_with_uns_nsm()
- sim_true_alignment()
- sim_twal_with_lns_nsm()
- sim_twal_with_same_n_mutation()
- sim_twal_with_std_nsm()
- sim_twal_with_uns_nsm()
- sim_twin_alignment()
- sim_yule_twin_tree()
- to_evidence_filename()
- to_twin_filename()
- to_twin_filenames()
- will_measure_evidence()
R Codes
- alignment_params_to_posterior_trees.R
- check_alignment.R
- check_alignment_params.R
- check_beast2_installed.R
- check_error_fun.R
- check_error_measure_params.R
- check_experiment.R
- check_experiments.R
- check_experiments_all_inference_models_are_unique.R
- check_experiments_candidates_have_same_beast2_files.R
- check_experiments_candidates_have_same_mcmcs.R
- check_gen_and_cand_save_to_different_files.R
- check_inference_conditions.R
- check_inference_model_type_names.R
- check_inference_model_weights.R
- check_init_pir_params.R
- check_is_ns_beast2_pkg_installed.R
- check_model_type.R
- check_mutation_rate.R
- check_pir_out.R
- check_pir_out_errors_above_zero.R
- check_pir_params.R
- check_pir_paramses.R
- check_reconstructed_phylogeny.R
- check_root_sequence.R
- check_sim_tral_fun.R
- check_sim_twal_fun.R
- check_sim_twin_tree_fun.R
- check_tree_and_model.R
- check_tree_and_models.R
- check_tree_and_model_errors.R
- check_tree_type.R
- check_tree_types.R
- check_twinning_params.R
- check_twinning_params_names.R
- check_twin_phylogeny.R
- collapse_tree_and_model.R
- collect_pir_outs.R
- combine_brts_and_topology.R
- combine_models.R
- complete_treelog_filename.R
- convert_pir_out_to_long.R
- copy_true_alignment.R
- count_n_mutations.R
- create_alignment_params.R
- create_all_bd_experiments.R
- create_all_coal_experiments.R
- create_all_experiments.R
- create_blocked_dna.R
- create_cand_experiment.R
- create_copy_twin_tree_from_true_fun.R
- create_error_measure_params.R
- create_exemplary_dd_tree.R
- create_exemplary_dd_tree_giappo.R
- create_experiment.R
- create_generative_trees.R
- create_gen_experiment.R
- create_inference_conditions.R
- create_mono_nuc_dna.R
- create_pir_params.R
- create_rate_matrix.R
- create_sim_yule_twin_tree_fun.R
- create_standard_mutation_rate.R
- create_std_pir_params.R
- create_std_pir_paramses.R
- create_test_cand_experiment.R
- create_test_experiment.R
- create_test_gen_experiment.R
- create_test_marg_liks.R
- create_test_phylogeny.R
- create_test_pir_params_setup.R
- create_test_pir_run_output.R
- create_tral_file.R
- create_tree_and_model_errors_from_folder.R
- create_tree_and_model_errors_from_folders.R
- create_true_alignment.R
- create_twal_file.R
- create_twinning_params.R
- create_twin_branching_times.R
- create_twin_tree.R
- default_params_doc.R
- delete_beast2_state_files.R
- errorses_to_data_frame.R
- est_evidences.R
- get_alignment_n_taxa.R
- get_alignment_sequences.R
- get_alignment_sequence_length.R
- get_copy_tral_fun.R
- get_experiments_filenames.R
- get_experiment_filenames.R
- get_gamma_error_fun.R
- get_model_selections.R
- get_nltt_error_fun.R
- get_pir_params_filenames.R
- get_pir_plot_fill_colors.R
- get_pir_plot_line_colors.R
- get_pir_plot_theme.R
- get_pir_plot_tree_and_model_descriptions.R
- get_remove_hex_twin_fun.R
- get_sim_bd_twin_tree_fun.R
- get_sim_tral_with_lns_site_model_fun.R
- get_sim_tral_with_std_nsm_fun.R
- get_sim_tral_with_uns_site_model_fun.R
- get_sim_twal_with_same_n_mutation_fun.R
- get_sim_twal_with_std_nsm_fun.R
- get_sim_yule_twin_tree_fun.R
- get_temp_errors_filename.R
- get_temp_evidence_filename.R
- get_temp_fasta_filename.R
- get_temp_tree_filename.R
- get_test_alignment.R
- get_tree_and_model_descriptions.R
- get_tree_and_model_values.R
- has_candidate_experiments.R
- has_twinning.R
- init_experiment.R
- init_pir_params.R
- is_best_candidate.R
- is_dna_seq.R
- is_pir_params.R
- phylo_to_errors.R
- pirouette.R
- pir_plot.R
- pir_plots.R
- pir_plot_from_file.R
- pir_plot_from_long.R
- pir_rename.R
- pir_rename_to_std.R
- pir_run.R
- pir_runs.R
- pir_run_distribution.R
- pir_run_true_tree.R
- pir_run_twin_tree.R
- pir_save.R
- pir_to_pics.R
- pir_to_tables.R
- plot_alignment_from_file.R
- read_errors_csv.R
- relevel_inference_model.R
- relevel_tree_and_model.R
- renum_rng_seeds.R
- replicate_pir_params.R
- rm_pir_param_files.R
- select_candidate_evidences.R
- select_experiments.R
- shorten_experiments.R
- shorten_pir_params.R
- shorten_pir_paramses.R
- sim_alignment_with_n_mutations.R
- sim_alignment_with_std_nsm.R
- sim_alignment_with_std_nsm_from_params.R
- sim_bd_twin_tree.R
- sim_tral_with_lns_site_model.R
- sim_tral_with_nsm.R
- sim_tral_with_uns_site_model.R
- sim_true_alignment.R
- sim_twal_with_lns_site_model.R
- sim_twal_with_nsm.R
- sim_twal_with_same_n_mutation.R
- sim_twal_with_uns_site_model.R
- sim_twin_alignment.R
- to_evidence_filename.R
- to_twin_filename.R
- to_twin_filenames.R
- twin_to_yule_tree.R
- utils-pipe.R
- utils.R
- will_measure_evidence.R
Selected R package: pirouette
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